FMO DATABASE

FMODB ID: R13N8

Calculation Name: 3DO9-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DO9

Chain ID: A

ChEMBL ID:

UniProt ID: Q81SV3

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	181
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1991908.129658
FMO2-HF: Nuclear repulsion	1915868.455232
FMO2-HF: Total energy	-76039.674426
FMO2-MP2: Total energy	-76260.518419

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:3:ACE )

Summations of interaction energy for fragment #1(A:3:ACE )

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-0.862	-0.487	0	-0.233	-0.142	0

Interaction energy analysis for fragmet #1(A:3:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.026

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].
3	A	5	VAL	0	0.087	0.067	3.881	0.092	0.467	-0.233	-0.142
4	A	6	SER	0	-0.035	-0.012	6.237	0.537	0.537	0.000	0.000
5	A	7	VAL	0	0.036	-0.007	7.564	0.066	0.066	0.000	0.000
6	A	8	ASN	0	-0.014	-0.029	10.900	0.053	0.053	0.000	0.000
7	A	9	GLU	-1	-0.844	-0.914	8.496	-1.236	-1.236	0.000	0.000
8	A	10	LYS	1	0.905	0.966	9.925	0.549	0.549	0.000	0.000
9	A	11	LYS	1	0.874	0.932	13.787	0.176	0.176	0.000	0.000
10	A	12	ASP	-1	-0.911	-0.961	15.767	-0.212	-0.212	0.000	0.000
11	A	13	PHE	0	0.030	0.037	15.746	0.023	0.023	0.000	0.000
12	A	14	VAL	0	-0.001	-0.003	17.538	0.031	0.031	0.000	0.000
13	A	15	LYS	1	0.966	0.980	19.930	0.163	0.163	0.000	0.000
14	A	16	TRP	0	-0.004	0.014	20.202	0.009	0.009	0.000	0.000
15	A	17	PHE	0	0.005	-0.002	21.498	0.021	0.021	0.000	0.000
16	A	18	LEU	0	-0.003	-0.022	23.162	0.016	0.016	0.000	0.000
17	A	19	ASN	0	-0.095	-0.043	25.410	0.021	0.021	0.000	0.000
18	A	20	ASN	0	-0.071	-0.029	25.189	0.010	0.010	0.000	0.000
19	A	21	TYR	0	-0.050	-0.021	24.292	0.006	0.006	0.000	0.000
20	A	22	GLN	0	0.015	0.018	28.653	0.000	0.000	0.000	0.000
21	A	23	LEU	0	0.000	-0.008	26.582	0.001	0.001	0.000	0.000
22	A	24	LYS	1	0.838	0.923	30.716	0.092	0.092	0.000	0.000
23	A	25	GLN	0	0.008	0.001	32.409	0.005	0.005	0.000	0.000
24	A	26	ARG	1	1.005	0.996	31.911	0.052	0.052	0.000	0.000
25	A	27	GLU	-1	-0.847	-0.941	32.033	-0.065	-0.065	0.000	0.000
26	A	28	CYS	0	-0.023	0.003	28.025	0.000	0.000	0.000	0.000
27	A	29	VAL	0	0.036	0.027	26.966	-0.010	-0.010	0.000	0.000
28	A	30	TRP	0	-0.010	-0.013	27.232	-0.003	-0.003	0.000	0.000
29	A	31	ILE	0	0.012	0.022	24.670	0.001	0.001	0.000	0.000
30	A	32	LEU	0	0.024	0.002	21.491	-0.003	-0.003	0.000	0.000
31	A	33	ASN	0	0.022	0.000	22.713	-0.013	-0.013	0.000	0.000
32	A	34	TYR	0	-0.018	0.002	24.382	0.008	0.008	0.000	0.000
33	A	35	LEU	0	-0.002	-0.004	19.940	0.006	0.006	0.000	0.000
34	A	36	MET	0	-0.022	-0.001	19.570	-0.009	-0.009	0.000	0.000
35	A	37	SER	0	-0.066	-0.012	20.269	0.004	0.004	0.000	0.000
36	A	38	HIS	0	-0.055	-0.030	20.926	0.021	0.021	0.000	0.000
37	A	39	ASP	-1	-0.816	-0.935	16.476	-0.072	-0.072	0.000	0.000
38	A	40	GLN	0	0.008	0.011	15.434	0.002	0.002	0.000	0.000
39	A	41	LEU	0	-0.078	-0.044	16.961	0.008	0.008	0.000	0.000
40	A	42	MET	0	0.000	-0.012	14.416	-0.028	-0.028	0.000	0.000
41	A	43	HIS	0	-0.016	-0.003	10.458	-0.067	-0.067	0.000	0.000
42	A	44	LYS	1	0.946	0.978	12.165	-0.012	-0.012	0.000	0.000
43	A	45	VAL	0	-0.029	0.016	14.916	-0.002	-0.002	0.000	0.000
44	A	46	HIS	1	0.803	0.896	11.083	0.239	0.239	0.000	0.000
45	A	47	PHE	0	0.025	0.010	13.897	0.070	0.070	0.000	0.000
46	A	48	VAL	0	0.022	0.015	14.924	-0.041	-0.041	0.000	0.000
47	A	49	GLU	-1	-0.799	-0.912	17.504	-0.207	-0.207	0.000	0.000
48	A	50	HIS	0	-0.036	-0.025	20.468	0.021	0.021	0.000	0.000
49	A	51	ALA	0	0.062	0.012	21.547	0.003	0.003	0.000	0.000
50	A	52	LYS	1	0.930	0.964	22.648	0.105	0.105	0.000	0.000
51	A	53	TYR	0	-0.045	-0.023	23.369	0.010	0.010	0.000	0.000
52	A	54	CYS	0	-0.064	0.002	20.208	0.001	0.001	0.000	0.000
53	A	55	PRO	0	0.052	0.031	21.106	0.005	0.005	0.000	0.000
54	A	56	ARG	1	0.884	0.937	21.915	0.077	0.077	0.000	0.000
55	A	57	GLY	0	0.015	0.030	22.116	-0.015	-0.015	0.000	0.000
56	A	58	LEU	0	-0.028	-0.013	22.776	0.014	0.014	0.000	0.000
57	A	59	VAL	0	0.012	0.008	23.493	-0.016	-0.016	0.000	0.000
58	A	60	MET	0	-0.018	-0.006	24.057	0.015	0.015	0.000	0.000
59	A	61	SER	0	0.014	0.006	26.504	-0.015	-0.015	0.000	0.000
60	A	62	ALA	0	0.010	0.002	28.408	0.007	0.007	0.000	0.000
61	A	63	ASN	0	-0.048	-0.045	30.137	-0.002	-0.002	0.000	0.000
62	A	64	CYS	0	-0.035	0.027	30.732	0.002	0.002	0.000	0.000
63	A	65	VAL	0	0.052	0.021	29.404	0.007	0.007	0.000	0.000
64	A	66	LYS	1	0.899	0.933	32.684	0.070	0.070	0.000	0.000
65	A	67	ASP	-1	-0.828	-0.900	30.248	-0.104	-0.104	0.000	0.000
66	A	68	THR	0	-0.005	-0.014	32.642	0.000	0.000	0.000	0.000
67	A	69	PRO	0	-0.026	-0.009	31.449	-0.006	-0.006	0.000	0.000
68	A	70	PHE	0	0.026	-0.003	27.829	-0.007	-0.007	0.000	0.000
69	A	71	HIS	0	0.008	0.020	29.204	0.007	0.007	0.000	0.000
70	A	72	PHE	0	-0.005	0.001	25.080	-0.007	-0.007	0.000	0.000
71	A	73	PHE	0	0.006	-0.017	26.286	0.007	0.007	0.000	0.000
72	A	74	LYS	1	0.924	0.972	26.319	0.046	0.046	0.000	0.000
73	A	75	GLN	0	0.024	-0.002	26.174	0.000	0.000	0.000	0.000
74	A	76	ASN	0	-0.001	0.011	28.778	0.000	0.000	0.000	0.000
75	A	77	VAL	0	-0.022	-0.003	31.715	0.001	0.001	0.000	0.000
76	A	78	MET	0	0.006	0.006	31.246	-0.005	-0.005	0.000	0.000
77	A	79	THR	0	-0.016	0.008	31.909	0.003	0.003	0.000	0.000
78	A	80	THR	0	0.048	0.001	32.386	-0.006	-0.006	0.000	0.000
79	A	81	ASP	-1	-0.879	-0.934	34.491	-0.051	-0.051	0.000	0.000
80	A	82	ALA	0	0.052	0.021	31.728	-0.001	-0.001	0.000	0.000
81	A	83	GLU	-1	-0.901	-0.950	31.935	-0.048	-0.048	0.000	0.000
82	A	84	LYS	1	0.927	0.972	33.950	0.037	0.037	0.000	0.000
83	A	85	SER	0	0.024	-0.004	29.437	0.001	0.001	0.000	0.000
84	A	86	PHE	0	-0.029	-0.016	27.304	-0.002	-0.002	0.000	0.000
85	A	87	HIS	0	-0.003	-0.011	29.687	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.861	-0.927	30.277	-0.036	-0.036	0.000	0.000
87	A	89	ILE	0	-0.114	-0.060	24.606	0.003	0.003	0.000	0.000
88	A	90	ARG	1	0.901	0.962	25.656	0.047	0.047	0.000	0.000
89	A	91	LEU	0	0.009	-0.005	27.612	0.004	0.004	0.000	0.000
90	A	92	ASN	0	-0.042	-0.022	26.063	0.001	0.001	0.000	0.000
91	A	93	ARG	1	0.889	0.964	23.192	0.035	0.035	0.000	0.000
92	A	94	ASP	-1	-0.903	-0.935	20.895	-0.018	-0.018	0.000	0.000
93	A	95	GLU	-1	-0.872	-0.951	20.262	-0.015	-0.015	0.000	0.000
94	A	96	ASP	-1	-0.911	-0.957	15.202	-0.096	-0.096	0.000	0.000
95	A	97	ILE	0	-0.095	-0.048	17.777	0.009	0.009	0.000	0.000
96	A	98	TYR	0	0.044	0.010	15.573	-0.018	-0.018	0.000	0.000
97	A	99	ILE	0	-0.009	-0.002	18.418	0.025	0.025	0.000	0.000
98	A	100	GLN	0	0.026	0.018	19.168	-0.022	-0.022	0.000	0.000
99	A	101	LEU	0	-0.018	-0.023	20.399	0.017	0.017	0.000	0.000
100	A	102	ASN	0	0.030	0.019	23.427	-0.018	-0.018	0.000	0.000
101	A	103	PHE	0	0.015	-0.006	21.197	0.019	0.019	0.000	0.000
102	A	104	LYS	1	0.958	0.960	26.711	0.095	0.095	0.000	0.000
103	A	105	SER	0	0.039	0.023	25.014	0.006	0.006	0.000	0.000
104	A	106	SER	0	0.028	0.009	22.927	-0.011	-0.011	0.000	0.000
105	A	107	PHE	0	-0.005	0.007	18.680	-0.021	-0.021	0.000	0.000
106	A	108	GLN	0	0.047	0.022	22.193	0.007	0.007	0.000	0.000
107	A	109	ASN	0	-0.026	-0.017	20.804	0.003	0.003	0.000	0.000
108	A	110	ALA	0	0.079	0.027	16.706	-0.019	-0.019	0.000	0.000
109	A	111	ASN	0	0.034	0.007	15.031	-0.052	-0.052	0.000	0.000
110	A	112	TYR	0	-0.002	-0.004	14.952	-0.053	-0.053	0.000	0.000
111	A	113	VAL	0	0.012	-0.005	15.375	-0.014	-0.014	0.000	0.000
112	A	114	ALA	0	-0.026	-0.003	11.258	-0.038	-0.038	0.000	0.000
113	A	115	VAL	0	-0.021	-0.005	10.678	-0.156	-0.156	0.000	0.000
114	A	116	LEU	0	-0.059	-0.017	12.609	0.029	0.029	0.000	0.000
115	A	117	GLU	-1	-0.835	-0.912	9.991	-0.679	-0.679	0.000	0.000
116	A	118	GLU	-1	-0.895	-0.958	11.829	-0.154	-0.154	0.000	0.000
117	A	119	ASN	0	-0.017	-0.015	13.736	0.042	0.042	0.000	0.000
118	A	120	PRO	0	0.002	0.010	15.301	0.015	0.015	0.000	0.000
119	A	121	TYR	0	0.040	0.003	17.875	0.031	0.031	0.000	0.000
120	A	122	LEU	0	-0.055	-0.029	20.918	0.010	0.010	0.000	0.000
121	A	123	PRO	0	-0.034	-0.007	22.681	0.006	0.006	0.000	0.000
122	A	124	LYS	1	1.039	0.973	25.449	0.078	0.078	0.000	0.000
123	A	125	HIS	0	-0.074	0.008	25.914	0.004	0.004	0.000	0.000
124	A	126	ILE	0	0.059	0.010	20.601	-0.006	-0.006	0.000	0.000
125	A	127	GLU	-1	-0.977	-0.978	23.667	-0.075	-0.075	0.000	0.000
126	A	128	VAL	0	0.038	0.035	21.264	0.001	0.001	0.000	0.000
127	A	129	ASN	0	-0.090	-0.063	19.572	-0.017	-0.017	0.000	0.000
128	A	130	GLU	-1	-0.830	-0.924	17.981	-0.155	-0.155	0.000	0.000
129	A	131	LYS	1	0.884	0.943	16.739	0.233	0.233	0.000	0.000
130	A	132	ASP	-1	-0.945	-0.968	11.897	-0.504	-0.504	0.000	0.000
131	A	133	ARG	1	0.962	0.973	14.916	0.143	0.143	0.000	0.000
132	A	134	LEU	0	-0.086	-0.030	17.101	0.011	0.011	0.000	0.000
133	A	135	LEU	0	0.026	0.018	14.719	0.017	0.017	0.000	0.000
134	A	136	ALA	0	-0.005	-0.013	17.392	0.009	0.009	0.000	0.000
135	A	137	GLU	-1	-0.889	-0.942	19.014	-0.138	-0.138	0.000	0.000
136	A	138	ARG	1	0.984	0.988	21.481	0.207	0.207	0.000	0.000
137	A	139	PHE	0	-0.038	-0.012	19.121	0.001	0.001	0.000	0.000
138	A	140	LEU	0	-0.024	-0.002	21.669	0.012	0.012	0.000	0.000
139	A	141	GLU	-1	-0.905	-0.958	23.726	-0.119	-0.119	0.000	0.000
140	A	142	GLU	-1	-0.831	-0.909	24.668	-0.131	-0.131	0.000	0.000
141	A	143	SER	0	-0.030	-0.017	23.105	0.007	0.007	0.000	0.000
142	A	144	VAL	0	-0.059	-0.025	25.761	0.012	0.012	0.000	0.000
143	A	145	PHE	0	0.004	0.010	28.644	0.011	0.011	0.000	0.000
144	A	146	SER	0	-0.031	-0.036	27.690	0.009	0.009	0.000	0.000
145	A	147	PHE	0	0.038	0.032	29.107	0.010	0.010	0.000	0.000
146	A	148	ARG	1	0.969	0.978	30.947	0.100	0.100	0.000	0.000
147	A	149	ARG	1	0.999	1.011	32.017	0.107	0.107	0.000	0.000
148	A	150	GLU	-1	-0.946	-0.974	31.411	-0.099	-0.099	0.000	0.000
149	A	151	ARG	1	0.819	0.921	34.612	0.079	0.079	0.000	0.000
150	A	152	LEU	0	0.050	-0.006	36.315	0.005	0.005	0.000	0.000
151	A	153	LEU	0	-0.014	-0.024	36.744	0.004	0.004	0.000	0.000
152	A	154	LYS	1	0.919	0.991	36.990	0.075	0.075	0.000	0.000
153	A	155	GLN	0	-0.029	-0.026	39.867	0.001	0.001	0.000	0.000
154	A	156	ILE	0	0.005	0.010	42.277	0.004	0.004	0.000	0.000
155	A	157	ASP	-1	-0.866	-0.933	42.732	-0.058	-0.058	0.000	0.000
156	A	158	GLU	-1	-0.946	-0.982	41.816	-0.057	-0.057	0.000	0.000
157	A	159	ALA	0	-0.055	-0.026	45.950	0.003	0.003	0.000	0.000
158	A	160	LEU	0	-0.066	-0.042	47.120	0.003	0.003	0.000	0.000
159	A	161	ASP	-1	-0.958	-0.962	48.260	-0.041	-0.041	0.000	0.000
160	A	162	LYS	1	0.905	0.954	46.821	0.048	0.048	0.000	0.000
161	A	163	GLN	0	-0.027	-0.010	52.238	0.002	0.002	0.000	0.000
162	A	164	ASP	-1	-0.838	-0.907	51.036	-0.038	-0.038	0.000	0.000
163	A	165	LYS	1	0.929	0.941	51.834	0.034	0.034	0.000	0.000
164	A	166	GLU	-1	-0.905	-0.969	52.770	-0.038	-0.038	0.000	0.000
165	A	167	ALA	0	0.014	0.009	47.956	-0.001	-0.001	0.000	0.000
166	A	168	PHE	0	0.040	0.041	48.143	-0.002	-0.002	0.000	0.000
167	A	169	HIS	0	-0.018	0.000	48.155	-0.001	-0.001	0.000	0.000
168	A	170	ARG	1	0.919	0.980	47.140	0.044	0.044	0.000	0.000
169	A	171	LEU	0	0.033	-0.009	43.180	-0.002	-0.002	0.000	0.000
170	A	172	THR	0	-0.031	-0.037	43.750	-0.003	-0.003	0.000	0.000
171	A	173	ALA	0	-0.065	-0.047	44.736	-0.002	-0.002	0.000	0.000
172	A	174	GLU	-1	-0.938	-0.959	42.282	-0.060	-0.060	0.000	0.000
173	A	175	LEU	0	-0.047	-0.024	39.464	-0.003	-0.003	0.000	0.000
174	A	176	LYS	1	0.927	0.973	40.123	0.048	0.048	0.000	0.000
175	A	177	MET	0	-0.033	0.000	39.707	0.000	0.000	0.000	0.000
176	A	178	LEU	0	-0.018	-0.015	35.007	-0.002	-0.002	0.000	0.000
177	A	179	GLU	-1	-0.905	-0.965	36.164	-0.078	-0.078	0.000	0.000
178	A	180	GLY	0	-0.049	-0.013	37.231	-0.001	-0.001	0.000	0.000
179	A	181	HIS	0	-0.052	-0.033	35.685	0.003	0.003	0.000	0.000
180	A	182	HIS	0	-0.127	-0.059	30.198	0.001	0.001	0.000	0.000
181	A	183	NME	0	0.026	0.034	29.563	0.003	0.003	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ACE )